Line a 9x9-inch baking pan with parchment, leaving an overhang on two sides for easy removal. Lightly grease the parchment so the bars release cleanly.
In a medium saucepan set over medium heat, combine the corn syrup and brown sugar. Stir constantly until the sugar dissolves and the mixture begins to steam and bubble lightly, about 3–4 minutes.
Remove the pan from the heat and whisk in the 6 tablespoons of butter until melted. Stir in the peanut butter until smooth, then whisk in the protein powder and vanilla extract to make a thick, glossy mixture.
Pour the peanut-butter mixture over the crispy rice cereal in a large bowl. Fold gently but thoroughly so every flake is coated—use a spatula and two motions to avoid crushing the cereal.
Transfer the coated cereal to the prepared pan and press it firmly and evenly into an even layer. For a compact surface, cover with another sheet of parchment and press with a flat-bottomed measuring cup. Chill in the refrigerator 10 minutes to help it set before topping.
While the base chills, melt the chocolate and butterscotch chips with 1 tablespoon butter. Use a microwave-safe bowl and heat in 20–25 second bursts, stirring between bursts until smooth; alternatively, melt gently over a double boiler. Stir in the teaspoon of vanilla at the end.
When the base is slightly firm but still tacky, pour the warm chocolate-butterscotch glaze over the bars and spread quickly with an offset spatula to an even layer. If desired, sprinkle a light pinch of flaky sea salt across the top to deepen the flavor.
Return the pan to the refrigerator and chill for another 15–20 minutes until the topping is fully set. Using the parchment overhang, lift the slab from the pan and place on a cutting board. Cut into 12 bars with a sharp knife (wipe the knife clean between cuts for tidy edges).
Store bars in an airtight container at room temperature for up to 3 days, or refrigerate up to 1 week. For longer storage, wrap individually and freeze up to 2 months.